Better comparison of couple of ontologies in an iterative process

src/fr/inrialpes/exmo/align/util/GroupAlign.java

@@ -273,7 +273,6 @@ public class GroupAlign {
 	Alignment init = null;
 	//OWLOntology onto1 = null;
 	//OWLOntology onto2 = null;
-	URI uri11 = null;
 
 	if ( urlprefix != null ){
 	    prefix = urlprefix+"/"+dir.getName()+"/";
@@ -292,10 +291,11 @@ public class GroupAlign {
 
 	BasicConfigurator.configure();
 	//System.err.println("Before: uri1= "+uri1+", uri11= "+uri11);
-	if ( uri1 == null ) {uri11 = new URI(prefix+source);}
-	else{uri11 = uri1;}
-	//System.err.println("After: uri1= "+uri1+", uri11= "+uri11);
+	if ( uri1 == null ) {uri1 = new URI(prefix+source);}
+	if (source != null && target != null){uri1 = new URI(prefix+source);}
+	//else{uri11 = uri1;}
 	URI uri2 = new URI(prefix+target);
+	System.err.println(" uri1= "+uri1+"\n uri2= "+uri2);
 
 	/*
 	handler = new OWLRDFErrorHandler() {
@@ -315,7 +315,7 @@ public class GroupAlign {
 	*/
 
 	if (debug > 1) System.err.println(" Handler set");
-	if (debug > 1) System.err.println(" URI1: "+uri11);
+	if (debug > 1) System.err.println(" URI1: "+uri1);
 	if (debug > 1) System.err.println(" URI2: "+uri2);
 	    
 	//try {
@@ -328,7 +328,7 @@ public class GroupAlign {
 		AlignmentParser aparser = new AlignmentParser(debug-1);
 		//init = aparser.parse( initName, loadedOntologies);
 		init = aparser.parse( initName );
-		uri11 = init.getFile1();
+		uri1 = init.getFile1();
 		uri2 = init.getFile2();
 		if (debug > 1) System.err.println(" Init parsed");
 	    }
@@ -343,7 +343,7 @@ public class GroupAlign {
 	    java.lang.reflect.Constructor alignmentConstructor =
 		alignmentClass.getConstructor(cparams);
 	    result = (AlignmentProcess)alignmentConstructor.newInstance(mparams);
-	    result.init( uri11, uri2 );
+	    result.init( uri1, uri2 );
 	    //result.setFile1(uri11);
 	    //result.setFile2(uri2);
 	} catch (Exception ex) {